EarlyGestation_SupplementaryFigures
Load packages
library(rmarkdown)
library(rmdformats)
library(dplyr)
library(readr)
library(stringr)
library(tidyr)
library(tibble)
library(magrittr)
library(ggplot2)
library(pheatmap)
library(ggrepel)
library(viridisLite)
library(DT)
library(cowplot)
library(here)
source(here("R/plot_expression.R"))
source(here("R/plot_proportions.R"))
source(here("R/plot_structures.R"))
source(here("R/get_profile_plot.R"))
oxygenGenes <- read_csv(here("data/oxygenGenes.csv.gz"))
oxygenTranscripts <- read_csv(here("data/oxygenTranscripts.csv.gz"))
dtelist <- read_rds(here("data/dtelist.rds"))
dgelist <- read_rds(here("data/dgelist.rds"))
dgelist$samples <- dgelist$samples %>%
mutate(GestationGroup = ifelse(GestationalAge <= 10,
paste0("6", "\U2012", "10"),
paste0("11", "\U2012", "23")
),
GestationGroup = factor(GestationGroup, levels = c(
paste0("6", "\U2012", "10"),
paste0("11", "\U2012", "23")
)))
dtelist$samples <- dtelist$samples %>%
mutate(GestationGroup = ifelse(GestationalAge <= 10,
paste0("6", "\U2012", "10"),
paste0("11", "\U2012", "23")
),
GestationGroup = factor(GestationGroup,
levels = c(paste0("6", "\U2012", "10"),
paste0("11", "\U2012", "23"))
)
)Figure S1 - Transcript Expression Volcano Plot
up <- oxygenTranscripts %>%
dplyr::filter(FDR < 0.05 & logFC >= 1)
down <- oxygenTranscripts %>%
dplyr::filter(FDR < 0.05 & logFC <= -1)
highlight1 <- oxygenTranscripts %>%
dplyr::filter(FDR < 0.01 & logFC > 3) %>%
arrange(desc(logFC)) %>%
mutate(direction = "up") %>%
head(5)
highlight2 <- oxygenTranscripts %>%
dplyr::filter(FDR < 0.01 & logFC < -3) %>%
arrange(desc(abs(logFC))) %>%
mutate(direction = "down") %>%
head(5)
highlight <- rbind(highlight1,
highlight2) %>%
distinct(GeneName, .keep_all = TRUE)
volcano <- oxygenTranscripts %>%
ggplot() +
geom_point(
colour = "grey",
aes(x = logFC,
y = -log10(FDR))
) +
geom_point(
data = up,
colour = "red",
aes(x = logFC,
y = -log10(FDR))
) +
geom_point(
data = down,
colour = "blue",
aes(x = logFC,
y = -log10(FDR))
) +
labs(x = "Log-fold change (logFC)",
y = "Significance (-log10 FDR)") +
ggtitle(
paste0("Differential Transcript Expression: 6",
"\U2012",
"10 weeks' vs 11-23 weeks' gestation")
) +
theme_bw() +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
volc_plot <- volcano +
geom_label_repel(data = highlight,
aes(x = logFC,
y = -log10(FDR),
label = TranscriptName,
colour = direction),
show.legend = FALSE) +
scale_colour_manual(values = c("blue", "red"))
volc_plot
Save the volcano supplementary figure
Figure S2 - FLT1, PGF, and IGF2
FLT1
flt_exp <- plot_txp(
dgelist = dtelist,
target_gene = "FLT1",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
flt_proportions <- plot_proportions(
dtelist = dtelist,
target_gene = "FLT1",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
strip.background = element_rect(fill = "lightblue"))
flt_legend <- cowplot::get_legend(
plot_proportions(
dtelist = dtelist,
target_gene = "FLT1",
variable = "GestationalAge",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
xlab("Gestational Age (weeks)") +
labs(fill = "Transcript") +
theme(legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black")))## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.flt_plot <- cowplot::plot_grid(flt_exp,
flt_proportions,
rel_heights = c(1, 1),
labels = c("A", "B", " "),
ncol = 2)
flt_cowplot <- cowplot::plot_grid(flt_plot,
flt_legend,
rel_widths = c(1, 0.2),
ncol = 2)
flt_cowplot
PGF
pgf_exp <- plot_txp(
dgelist = dtelist,
target_gene = "PGF",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
pgf_proportions <- plot_proportions(
dtelist = dtelist,
target_gene = "PGF",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
axis.text.x = element_text(angle = 45,
vjust = 0.6),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black"),
strip.background = element_rect(fill = "lightblue"))
pgf_legend <- cowplot::get_legend(
plot_proportions(
dtelist = dtelist,
target_gene = "PGF",
variable = "GestationalAge",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
xlab("Gestational Age (weeks)") +
labs(fill = "Transcript") +
theme(legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black")))## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.pgf_plot <- cowplot::plot_grid(pgf_exp,
pgf_proportions,
rel_heights = c(1, 1),
labels = c("C", "D", " "),
ncol = 2)
pgf_cowplot <- cowplot::plot_grid(pgf_plot,
pgf_legend,
rel_widths = c(1, 0.2),
ncol = 2)
pgf_cowplot
IGF2
igf_exp <- plot_txp(
dgelist = dtelist,
target_gene = "IGF2",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
igf_proportions <- plot_proportions(
dtelist = dtelist,
target_gene = "IGF2",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
axis.text.x = element_text(angle = 45,
vjust = 0.6),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
strip.background = element_rect(fill = "lightblue"))
igf_legend <- cowplot::get_legend(
plot_proportions(
dtelist = dtelist,
target_gene = "IGF2",
variable = "GestationalAge",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
xlab("Gestational Age (weeks)") +
labs(fill = "Transcript") +
theme(legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black")))## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.
Figure S3 - Transcript proportions
CD36 Proportions
fig3_cd36_dtelist <- dtelist
fig3_cd36_dtelist$genes$transcript_name %<>%
str_replace(pattern = "CD36-016",
replacement = "CD36-016*")
cd36_prop <- plot_proportions(
dtelist = fig3_cd36_dtelist,
target_gene = "CD36",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
labs(x = "Gestation Group (weeks)",
fill = "Transcript") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
strip.background = element_rect(fill = "lightblue"),
strip.text = element_text(size = 20, colour = "black"),
legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black"))
cd36_prop
NRP2 Proportions
fig3_nrp2_dtelist <- dtelist
fig3_nrp2_dtelist$genes$transcript_name %<>%
str_replace(pattern = "NRP2-005",
replacement = "NRP2-005*")
nrp2_prop <- plot_proportions(
dtelist = fig3_nrp2_dtelist,
target_gene = "NRP2",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
labs(x = "Gestation Group (weeks)",
fill = "Transcript") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
strip.background = element_rect(fill = "lightblue"),
strip.text = element_text(size = 20, colour = "black"),
legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black"))
nrp2_prop
Figure S4 - Transcript Expression
CD36 Transcript Expression
cd36_dte <- dtelist
cd36_dte$genes$transcript_name %<>%
str_replace(pattern = "CD36-006", replacement = "CD36-006*") %>%
str_replace(pattern = "CD36-014", replacement = "CD36-014*") %>%
str_replace(pattern = "CD36-017", replacement = "CD36-017*") %>%
str_replace(pattern = "CD36-015", replacement = "CD36-015*") %>%
str_replace(pattern = "CD36-021", replacement = "CD36-021*") %>%
str_replace(pattern = "CD36-016", replacement = "CD36-016*")
cd36_exp <- plot_txp(
dgelist = cd36_dte,
target_gene = "CD36",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)",
fill = "Transcript",
colour = "Transcript") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black"))
cd36_exp## Warning: Removed 11 rows containing non-finite outside the scale range
## (`stat_smooth()`).
NUCB2 Transcript Expression
nucb_dte <- dtelist
nucb_dte$genes$transcript_name %<>%
str_replace(pattern = "NUCB2-002", replacement = "NUCB2-002*") %>%
str_replace(pattern = "NUCB2-012", replacement = "NUCB2-012*") %>%
str_replace(pattern = "NUCB2-005", replacement = "NUCB2-005*") %>%
str_replace(pattern = "NUCB2-017", replacement = "NUCB2-017*") %>%
str_replace(pattern = "NUCB2-201", replacement = "NUCB2-201*") %>%
str_replace(pattern = "NUCB2-006", replacement = "NUCB2-006*")
nucb2_exp <- plot_txp(
dgelist = nucb_dte,
target_gene = "NUCB2",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)",
colour = "Transcript",
fill = "Transcript") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"),
legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black"))
nucb2_exp## Warning: Removed 2 rows containing non-finite outside the scale range
## (`stat_smooth()`).
Full Plot
## Warning: Removed 11 rows containing non-finite outside the scale range
## (`stat_smooth()`).## Warning: Removed 2 rows containing non-finite outside the scale range
## (`stat_smooth()`).
Now save the plot
Figure S5 - Gene Heatmap
First prepare the data for heatmap visualisation
scale_rows <- function(x){
m = apply(x, 1, mean, na.rm = T)
s = apply(x, 1, sd, na.rm = T)
return((x - m) / s)
}
gene_tx_diff <- read_csv(here("data/figure3_transcripts.csv"))
clusterOrder <- dgelist %>%
cpm() %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
dplyr::filter(Gene %in% gene_tx_diff$Gene) %>%
dplyr::arrange(Gene) %>%
set_rownames(gene_tx_diff %>%
dplyr::filter(!Gene == "ENST00000372728") %>%
dplyr::arrange(Gene) %>%
dplyr::select(Gene) %>%
as.matrix() %>%
as.character()) %>%
dplyr::select(-Gene) %>%
as.matrix() %>%
dist() %>%
hclust() %>%
as.dendrogram(method = "ward.D2") %>%
order.dendrogram()
scaled_cpm <- dgelist %>%
cpm(log = TRUE) %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
dplyr::filter(Gene %in% gene_tx_diff$Gene) %>%
dplyr::arrange(Gene) %>%
set_rownames(gene_tx_diff %>%
dplyr::filter(!Gene == "ENST00000372728") %>%
dplyr::arrange(Gene) %>%
dplyr::select(Gene) %>%
as.matrix() %>%
as.character()) %>%
dplyr::select(-Gene) %>%
as.matrix()Added a space in "Gestation Group " to make sure the
legend title and legend bar do not overlap
clusteredMatrix <- scaled_cpm[clusterOrder, ]
clusteredMatrix <- clusteredMatrix[, (dgelist$samples %>%
dplyr::arrange(GestationalAge) %>%
dplyr::filter(
ID %in% colnames(dgelist)
) %>%
dplyr::arrange(GestationalAge) %>%
dplyr::select(ID) %>%
as.matrix() %>%
as.character)]
gene_row_order <- c("GDPD5", "MGAT1", "ITSN1", "AZIN1",
"ADAM10", "HBA2", "SLC16A3", "PSG9",
"CALM1", "MTUS1", "VMP1", "RPS24",
"PSG5", "FLT1", "TFPI2")
gene_order <- oxygenGenes %>%
dplyr::select("Gene",
"GeneName") %>%
dplyr::filter(GeneName %in% gene_row_order) %>%
distinct() %>%
column_to_rownames("GeneName")
clusteredMatrix <- clusteredMatrix %>%
as.data.frame() %>%
rownames_to_column(var = "Gene") %>%
left_join(oxygenGenes %>%
dplyr::select("Gene",
"GeneName"),
by = "Gene") %>%
dplyr::select(-Gene) %>%
column_to_rownames("GeneName") %>%
as.matrix()
ann_col <- dgelist$samples %>%
dplyr::select(ID, "Gestation Group " = Timepoint) %>%
as.data.frame() %>%
set_rownames(dgelist$samples$ID) %>%
dplyr::select("Gestation Group ")
dgelist$samples %>%
dplyr::arrange(GestationalAge) %>%
datatable()And now plot the final heatmap
pheatmap(clusteredMatrix[gene_row_order, ],
color = plasma(84),
border_color = NA,
show_colnames = FALSE,
cluster_cols = FALSE,
cluster_rows = FALSE,
gaps_col = 27,
gaps_row = c(3,8,13),
annotation_col = ann_col)
pheatmap(clusteredMatrix,
color = plasma(84),
border_color = NA,
show_colnames = FALSE,
cluster_cols = FALSE,
cutree_rows = 4,
main = paste0("Genes with the greatest differences\n",
"in expression to their transcripts"),
fontsize = 16,
gaps_col = 27,
annotation_col = ann_col)
Figure S6 - FN1 and PSG9
FN1
fn1_gene <- plot_txp(
dgelist = dgelist,
target_gene = "FN1",
variable = "GestationalAge",
level = "gene",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
fn1_tx <- plot_txp(
dgelist = dtelist,
target_gene = "FN1",
variable = "GestationalAge",
level = "transcript",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
fn1_legend <- cowplot::get_legend(
plot_txp(
dgelist = dtelist,
target_gene = "FN1",
variable = "GestationalAge",
level = "transcript",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
colour = "Transcript",
fill = "Transcript") +
theme(legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black")
)
)## Warning: Removed 6 rows containing non-finite outside the scale range
## (`stat_smooth()`).## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.top_row <- cowplot::plot_grid(fn1_gene,
fn1_tx,
fn1_legend,
nrow = 1,
rel_widths = c(1, 1, 0.4),
labels = c("A", "B", ""))## Warning: Removed 6 rows containing non-finite outside the scale range
## (`stat_smooth()`).
PSG9
psg9_gene <- plot_txp(
dgelist = dgelist,
target_gene = "PSG9",
variable = "GestationalAge",
level = "gene",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
psg9_tx <- plot_txp(
dgelist = dtelist,
target_gene = "PSG9",
variable = "GestationalAge",
level = "transcript",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 20,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 22,
colour = "black",
face = "bold"))
psg9_legend <- cowplot::get_legend(
plot_txp(
dgelist = dtelist,
target_gene = "PSG9",
variable = "GestationalAge",
level = "transcript",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
colour = "Transcript",
fill = "Transcript") +
theme(legend.title = element_text(size = 20,
colour = "black",
face = "bold"),
legend.text = element_text(size = 18,
colour = "black"))
)## Warning: Removed 6 rows containing non-finite outside the scale range
## (`stat_smooth()`).## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.bottom_row <- cowplot::plot_grid(psg9_gene,
psg9_tx,
psg9_legend,
nrow = 1,
rel_widths = c(1, 1, 0.4),
labels = c("C", "D", ""))## Warning: Removed 6 rows containing non-finite outside the scale range
## (`stat_smooth()`).
Figure S7 - VMP1 profile
I used 1300x1000 for figures s7-s10
VMP1 TxProfileR
vmp1 <- txprofiler(
dgelist = dgelist,
dtelist = dtelist,
target_gene = "VMP1",
variable = "GestationalAge",
transcript_variable = "GestationalAge",
dtu_variable = "GestationGroup",
abundance_path = here("data/salmon_abundance.csv.gz"),
tpm_method = "tximport",
gene_x_label = "Gestational Age (weeks)",
transcript_x_label = "Gestational Age (weeks)",
dtu_x_label = "Gestation Group (weeks)",
plot_title_size = 30
)## Warning: `select_()` was deprecated in dplyr 0.7.0.
## ℹ Please use `select()` instead.
## ℹ The deprecated feature was likely used in the wiggleplotr package.
## Please report the issue to the authors.
## This warning is displayed once every 8 hours.
## Call `lifecycle::last_lifecycle_warnings()` to see where this warning was
## generated.## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.
Save the plot
Figure S8 - ASAH1 profile
ASAH1 TxProfileR
asah1 <- txprofiler(
dgelist = dgelist,
dtelist = dtelist,
target_gene = "ASAH1",
variable = "GestationalAge",
transcript_variable = "GestationalAge",
dtu_variable = "GestationGroup",
abundance_path = here("data/salmon_abundance.csv.gz"),
tpm_method = "tximport",
gene_x_label = "Gestational Age (weeks)",
transcript_x_label = "Gestational Age (weeks)",
dtu_x_label = "Gestation Group (weeks)",
plot_title_size = 30
)## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.
Save the plot
Figure S9 - GPR126 profile
GPR126 TxProfileR
gpr126 <- txprofiler(
dgelist = dgelist,
dtelist = dtelist,
target_gene = "GPR126",
variable = "GestationalAge",
transcript_variable = "GestationalAge",
dtu_variable = "GestationGroup",
abundance_path = here("data/salmon_abundance.csv.gz"),
tpm_method = "tximport",
gene_x_label = "Gestational Age (weeks)",
transcript_x_label = "Gestational Age (weeks)",
dtu_x_label = "Gestation Group (weeks)",
plot_title_size = 36,
axis_title_size = 24,
axis_text_size = 14,
legend_title_size = 24,
legend_text_size = 22,
strip_text_size = 10
)## Warning: Removed 1 row containing non-finite outside the scale range (`stat_smooth()`).
## Removed 1 row containing non-finite outside the scale range (`stat_smooth()`).## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.
Save the plot
Figure S10 - TFPI2 profile
TFPI2 TxProfileR
tfpi2 <- txprofiler(
dgelist = dgelist,
dtelist = dtelist,
target_gene = "TFPI2",
variable = "GestationalAge",
transcript_variable = "GestationalAge",
dtu_variable = "GestationGroup",
abundance_path = here("data/salmon_abundance.csv.gz"),
tpm_method = "tximport",
gene_x_label = "Gestational Age (weeks)",
transcript_x_label = "Gestational Age (weeks)",
dtu_x_label = "Gestation Group (weeks)",
plot_title_size = 30
)## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.
Save the plot
Figure S11 - MTUS1, PTPRJ, RPS24, and PSG6
MTUS1
mtus1_exp <- plot_txp(
dgelist = dtelist,
target_gene = "MTUS1",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"))
mtus1_prop <- plot_proportions(
dtelist = dtelist,
target_gene = "MTUS1",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)",
fill = "Transcript") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"),
strip.text = element_text(size = 20,
colour = "black"),
strip.background = element_rect(fill = "lightblue"))
mtus1_legend <- cowplot::get_legend(
plot_txp(
dgelist = dtelist,
target_gene = "MTUS1",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
fill = "Transcript",
colour = "Transcript") +
theme(legend.title = element_text(size = 24,
colour = "black",
face = "bold"),
legend.text = element_text(size = 22,
colour = "black"))
) ## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.first_col <- cowplot::plot_grid(
mtus1_exp,
mtus1_prop,
mtus1_legend,
labels = c("A", "B", ""),
ncol = 3,
rel_widths = c(1, 1, 0.3)
)
first_col
PTPRJ
ptprj_exp <- plot_txp(
dgelist = dtelist,
target_gene = "PTPRJ",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"))
ptprj_prop <- plot_proportions(
dtelist = dtelist,
target_gene = "PTPRJ",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)",
fill = "Transcript") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"),
strip.text = element_text(size = 20,
colour = "black"),
strip.background = element_rect(fill = "lightblue"))
ptprj_legend <- cowplot::get_legend(
plot_txp(
dgelist = dtelist,
target_gene = "PTPRJ",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
fill = "Transcript",
colour = "Transcript") +
theme(legend.title = element_text(size = 24,
colour = "black",
face = "bold"),
legend.text = element_text(size = 22,
colour = "black"))
)## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.second_col <- cowplot::plot_grid(
ptprj_exp,
ptprj_prop,
ptprj_legend,
labels = c("C", "D", ""),
ncol = 3,
rel_widths = c(1, 1, 0.3)
)
second_col
RPS24
rps24_exp <- plot_txp(
dgelist = dtelist,
target_gene = "RPS24",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"))
rps24_prop <- plot_proportions(
dtelist = dtelist,
target_gene = "RPS24",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)",
fill = "Transcript") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"),
strip.text = element_text(size = 20,
colour = "black"),
strip.background = element_rect(fill = "lightblue"))
rps24_legend <- cowplot::get_legend(
plot_txp(
dgelist = dtelist,
target_gene = "RPS24",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
fill = "Transcript",
colour = "Transcript") +
theme(legend.title = element_text(size = 24,
colour = "black"),
legend.text = element_text(size = 22,
colour = "black"))
)## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.third_col <- cowplot::plot_grid(
rps24_exp,
rps24_prop,
rps24_legend,
labels = c("E", "F", ""),
ncol = 3,
rel_widths = c(1, 1, 0.3)
)
third_col
PSG6
psg6_exp <- plot_txp(
dgelist = dtelist,
target_gene = "PSG6",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = FALSE
) +
labs(x = "Gestational Age (weeks)",
y = "Transcript Expression (log2 TPM)") +
theme(axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 22,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"))
psg6_prop <- plot_proportions(
dtelist = dtelist,
target_gene = "PSG6",
variable = "GestationGroup",
tpm_method = "tximport",
path = here("data/salmon_abundance.csv.gz"),
keep_legend = FALSE
) +
labs(x = "Gestation Group (weeks)",
fill = "Transcript") +
theme(axis.text.x = element_text(angle = 45, vjust = 0.6),
axis.title = element_text(size = 24,
colour = "black"),
axis.text = element_text(size = 18,
colour = "black"),
plot.title = element_text(size = 26,
colour = "black",
face = "bold"),
strip.text = element_text(size = 11,
colour = "black"),
strip.background = element_rect(fill = "lightblue"))
psg6_legend <- cowplot::get_legend(
plot_txp(
dgelist = dtelist,
target_gene = "PSG6",
variable = "GestationalAge",
level = "transcript",
tpm_method = "standard",
path = NULL,
keep_legend = TRUE
) +
labs(x = "Gestational Age (weeks)",
fill = "Transcript",
colour = "Transcript") +
theme(legend.title = element_text(size = 24,
colour = "black"),
legend.text = element_text(size = 22,
colour = "black"))
)## Warning: Removed 1 row containing non-finite outside the scale range
## (`stat_smooth()`).## Warning in get_plot_component(plot, "guide-box"): Multiple components found;
## returning the first one. To return all, use `return_all = TRUE`.fourth_col <- cowplot::plot_grid(
psg6_exp,
psg6_prop,
psg6_legend,
labels = c("G", "H", ""),
ncol = 3,
rel_widths = c(1, 1, 0.3)
)## Warning: Removed 1 row containing non-finite outside the scale range
## (`stat_smooth()`).
